Baboons are an important biomedical model for many complex traits, including athlerosclerosis, bone density and obesity. With short generation times and an ability to control the environment, baboons provide a natural complement to human genetic studies of complex traits. However, high-resolution genetic studies in baboons are hampered by a lack of genomic resources. We will address this gap by improving the quality of the baboon genome assembly, providing comprehensive maps of common polymorphisms and haplotypes across the baboon genome, and constructing a high-resolution genetic map for baboons. Together, these resources will enable future fine-scale genotype-phenotype studies in baboons, which in turn may lead to important biomedical advances in understanding the genetic basis of human disease.